Unpaired data as a first-order challenge in single-cell and spatial proteomics - @mkoutrouli.bsky.social @panosroussos.bsky.social @scverse.bsky.social go.nature.com/3NHDkGP
Mikaela Koutrouli
@mkoutrouli.bsky.social
Computing all things single-cell | Postdoc at Genentech @MarioniLab | Steering council at scverse.org
Two inspiring days in Berlin just wrapped up with our scverse hackathon on single-cell and spatial proteomics and it’s hard not to feel energized by what this community can do together.
It’s finally time to welcome someone new into our mission. We’re hiring a Community Manager to help shape and support the growing scverse ecosystem. This is a position we’ve been looking forward to and I couldn’t be more excited to pass this opportunity on to someone new.
scverse@scverse.bsky.social · 9mo agoWe’re looking for a Community Manager to help shape and support the growing scverse ecosystem. Deadline January 10, 2026! More details here: jobs.helmholtz-muenchen.de/jobposting/d...
Excited to share new preprint led by Sergio Salas on “unassigned RNAs” in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns. 📄 www.biorxiv.org/content/10.6...
Proud to close out an incredible year with an update on where scverse is today and where we’re heading. I’d love for you to join me, share your ideas, challenge us, and help shape what comes next. It’s time! 💪
scverse@scverse.bsky.social · 9mo agoWe will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST! Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse! Zoom registration link for the meeting: lnkd.in/dZpbKKsY
As more single-cell perturbation data become available, it is crucial to establish a consensus on measures of success for perturbation prediction models. I reviewed recent literature and collected some thoughts on the current state of affairs. open.substack.com/pub/giovanni...
Virtual Cell Perturbation Metrics Reloaded
Thoughts on metrics for perturbation prediction models
open.substack.com
We wrapped up an inspiring week with a visit to NVIDIA headquarters right after the scverse conference. Huge thanks to the NVIDIA Healthcare team and @severin7.bsky.social for hosting us and for the great discussions on scaling single-cell analysis and accelerating open science ⚡️
We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST! Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI! More information and Zoom registration link in 🧵
scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄
It’s rare to have the core of innovation in one place, but the scverse conference 2025 made it happen. @biohub.org x NVIDIA x @scverse.bsky.social : three forces, one room, endless acceleration.
What a suitable moment to have a community meeting by @maltekuehl.com and @biocontext.ai! Since we didn’t manage to have him on the conference, join us next Tuesday! 💪❤️
scverse@scverse.bsky.social · 10mo agoWe will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST! Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI! More information and Zoom registration link in 🧵
John Marioni at the @scverse.bsky.social conference 2025! “Make sure you understand first when complex methods are valuable” 💪
🤖🧬 New biomedical MCP server added to the registry: anndata-mcp Check it out at https://biocontext.ai/registry/biocontext-ai/anndata-mcp
We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST! Eric Armingol will be presenting on scCellFie! More information and Zoom registration link in 🧵
You asked, we delivered! Online participation is now live.
scverse@scverse.bsky.social · 10mo agoWe're pleased to announce that we are now offering online attendance via Zoom. Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co.... We hope to see you online at the conference!
We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST! Eric Armingol will be presenting on scCellFie! More information and Zoom registration link in 🧵
We will have our next community meeting on Tuesday, 2025-10-28 at 18:00 CEST! @kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist. (Zoom registration link and more information in thread!) 🧵
How amazing that Genentech supports us and will have such a strong representation at the @scverse.bsky.social conference! 🙏
scverse@scverse.bsky.social · 11mo ago🌟 Thank You to Our Gold Sponsor: Genentech! 🌟 We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆 #scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
How amazing that Genentech supports us and will have such a strong representation at the @scverse.bsky.social conference! 🙏
🌟 Thank You to Our Silver Sponsor: Proteintech! 🌟 We're excited to recognize Proteintech as a Silver Sponsor of scverse conference 2025! 🥈 @proteintech.bsky.social #scverse2025 #Proteintech #ComputationalBiology #SingleCell #Antibodies #ProteomicsTools #SpatialOmics #Bioinformatics
👉 and make sure not to miss the one-and-only Romain Lopez's talk about PhenoBridge, our joint work on ML approaches to integrate perturb-seq and genetic association data (Wed 10.45am) Come find me or just reach out if you'd like to chat! [2/2]
While the conference is underway, business as usual! 💪
scverse@scverse.bsky.social · 11mo agoWe will have our next community meeting on Tuesday, 2025-10-14 at 18:00 CEST! Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis. (Zoom registration link and more information in thread!) 🧵
Last chance for the early-bird 🐣 Join us!
scverse@scverse.bsky.social · 11mo agoLast call, scverse community! 🐦 Early-bird closes October 17 for the scverse Conference 2025. Single-cell, open science, and the people behind it — all in one place. 📝 Register here: www.eventbrite.com/e/scverse-co... 2 days of talks + 1 day of workshops ℹ️ Info: scverse.org/conference2025
🌟 Thank You to Our Gold Sponsor: Stellaromics! 🌟 We're proud to recognize Stellaromics as a Gold Sponsor of scverse conference 2025! 🥇 @stellaromics.bsky.social #scverse2025 #SpatialBiology #3DSpatial #ComputationalBiology #SingleCell #Stellaromics #SpatialOmics #Bioinformatics
We will have our next community meeting on Tuesday, 2025-10-14 at 18:00 CEST! Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis. (Zoom registration link and more information in thread!) 🧵
ICYMI! 🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀 We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025! More information in 🧵 #scverse2025 #Bioinformatics #AgenticAI #Conference
🤖🧬 New biomedical MCP server added to the registry: OMOP MCP Server Check it out at https://biocontext.ai/registry/OHNLP/omop_mcp
Fantastic lineup of panelists to discuss everything agentic coding in bioinformatics, still time to register here: www.eventbrite.com/e/scverse-co...
Scverse Conference 2025
From the foundational open-source software in the life sciences — to its large community coming together
eventbrite.com
scverse@scverse.bsky.social · 11mo ago🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀 We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025! More information in 🧵 #scverse2025 #Bioinformatics #AgenticAI #Conference
Can’t wait 😱
scverse@scverse.bsky.social · 11mo ago🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀 We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025! More information in 🧵 #scverse2025 #Bioinformatics #AgenticAI #Conference